I just tried it on a few and while it was able to generate the nii files it failed to generate the bval/bvec files I'm looking for. Is it not typical behavior for mri_convert to generate bval/bvec files for DTI runs or is this an error?

Graham
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edu]
Sent: Wednesday, February 08, 2017 10:15 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] dcm2niix

Hi Graham – Have you tried mri_convert? The 6.0 version should be able to extract diffusion gradient tables and b-value tables from most standard recent dicoms.

a.y

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Warner, Graham Cary" <GWARNER@mgh.harvard.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, February 8, 2017 at 10:01 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] dcm2niix

Hi all,

Can we get dcm2niix added to the system instance of fsl? It can't find it in 5.0.7 or 5.0.9 (please let me know if it is somewhere else and I'm just not seeing it). I'm having problems generating .bval and .bvec files from certain DTI datasets using dcm2nii and the NITRC guys told me I should be using dcm2niix.

Thanks,
Graham